Low PWM's on throttle in AUTO mode

Dear All,
I have had this peculiar response from my pixhawk today in Auto and Loiter mode.
During ground testing, the throttle goes to maximum in AUTO mode and throttle maintains RC PWM during MANUAL or FBWA mode.
During flight, the throttle went to idle when i went to LOITER mode or AUTO mode.
After reading the logs, i realized that the throttle servo was in opposite direction (low PWM means full throttle and high PWM means idle throttle). I did the radio calibration before the flight and it was reversed like this as well but i thought since i have taught the pixhawk whats low and whats high, the FMU manages the PWM’s accordingly.
Please help. I have attached the logs for the flight below: